Starting phenix.real_space_refine on Tue May 5 02:16:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovw_70925/05_2026/9ovw_70925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovw_70925/05_2026/9ovw_70925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ovw_70925/05_2026/9ovw_70925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovw_70925/05_2026/9ovw_70925.map" model { file = "/net/cci-nas-00/data/ceres_data/9ovw_70925/05_2026/9ovw_70925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovw_70925/05_2026/9ovw_70925.cif" } resolution = 4.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 16004 2.51 5 N 4196 2.21 5 O 4616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24938 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6240 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 26, 'TRANS': 759} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6203 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 767} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 10.12, per 1000 atoms: 0.41 Number of scatterers: 24938 At special positions: 0 Unit cell: (143.64, 131.67, 188.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 4616 8.00 N 4196 7.00 C 16004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.05 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 28 sheets defined 44.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.793A pdb=" N GLN A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 4.207A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 170 through 181 removed outlier: 3.856A pdb=" N ARG A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 208 removed outlier: 3.683A pdb=" N ALA A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.684A pdb=" N GLU A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.569A pdb=" N ILE A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.973A pdb=" N VAL A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 419 through 429 removed outlier: 4.045A pdb=" N ALA A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 removed outlier: 3.675A pdb=" N GLU A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 520 through 543 removed outlier: 3.914A pdb=" N CYS A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.621A pdb=" N SER A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 596 through 626 removed outlier: 3.786A pdb=" N ILE A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.087A pdb=" N ARG A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.524A pdb=" N GLY A 685 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 710 removed outlier: 5.360A pdb=" N TYR A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 708 " --> pdb=" O MET A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 removed outlier: 3.887A pdb=" N GLU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 763 removed outlier: 3.824A pdb=" N TRP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 800 Processing helix chain 'A' and resid 800 through 811 removed outlier: 3.525A pdb=" N ILE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 815 removed outlier: 4.269A pdb=" N ARG A 815 " --> pdb=" O TYR A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.518A pdb=" N ARG B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.865A pdb=" N LEU B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.130A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 4.084A pdb=" N VAL B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 removed outlier: 4.068A pdb=" N PHE B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.840A pdb=" N VAL B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.244A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.630A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.712A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.950A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.509A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.921A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 576 removed outlier: 3.591A pdb=" N SER B 576 " --> pdb=" O ILE B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 576' Processing helix chain 'B' and resid 577 through 585 removed outlier: 4.004A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.964A pdb=" N ARG B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.637A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 4.271A pdb=" N LEU B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 786 removed outlier: 3.878A pdb=" N SER B 785 " --> pdb=" O GLU B 782 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 786 " --> pdb=" O LYS B 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 782 through 786' Processing helix chain 'B' and resid 794 through 819 removed outlier: 4.051A pdb=" N LEU B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 800 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 54 through 68 removed outlier: 3.793A pdb=" N GLN C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 4.207A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 92 " --> pdb=" O PHE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 170 through 181 removed outlier: 3.857A pdb=" N ARG C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 208 removed outlier: 3.684A pdb=" N ALA C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU C 207 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 4.684A pdb=" N GLU C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 261 removed outlier: 3.568A pdb=" N ILE C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 298 removed outlier: 3.973A pdb=" N VAL C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 296 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 331 Processing helix chain 'C' and resid 419 through 429 removed outlier: 4.045A pdb=" N ALA C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 removed outlier: 3.675A pdb=" N GLU C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 520 through 543 removed outlier: 3.914A pdb=" N CYS C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL C 534 " --> pdb=" O ILE C 530 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 541 " --> pdb=" O PHE C 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 581 removed outlier: 3.620A pdb=" N SER C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 596 Processing helix chain 'C' and resid 596 through 626 removed outlier: 3.785A pdb=" N ILE C 607 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE C 608 " --> pdb=" O PHE C 604 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 609 " --> pdb=" O THR C 605 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 removed outlier: 4.087A pdb=" N ARG C 656 " --> pdb=" O LYS C 652 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 681 through 692 removed outlier: 3.523A pdb=" N GLY C 685 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 690 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 692 " --> pdb=" O ARG C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 710 removed outlier: 5.359A pdb=" N TYR C 707 " --> pdb=" O THR C 703 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 752 removed outlier: 3.887A pdb=" N GLU C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 763 removed outlier: 3.823A pdb=" N TRP C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 800 Processing helix chain 'C' and resid 800 through 811 removed outlier: 3.525A pdb=" N ILE C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 815 removed outlier: 4.269A pdb=" N ARG C 815 " --> pdb=" O TYR C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 812 through 815' Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.518A pdb=" N ARG D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 84 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.865A pdb=" N LEU D 92 " --> pdb=" O PHE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.129A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 4.084A pdb=" N VAL D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 removed outlier: 4.068A pdb=" N PHE D 181 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.841A pdb=" N VAL D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 237 removed outlier: 4.244A pdb=" N PHE D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.630A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.712A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.950A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.510A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.921A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 576 removed outlier: 3.591A pdb=" N SER D 576 " --> pdb=" O ILE D 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 573 through 576' Processing helix chain 'D' and resid 577 through 585 removed outlier: 4.004A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.965A pdb=" N ARG D 599 " --> pdb=" O SER D 595 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 754 removed outlier: 3.637A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 removed outlier: 4.270A pdb=" N LEU D 762 " --> pdb=" O VAL D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 786 removed outlier: 3.879A pdb=" N SER D 785 " --> pdb=" O GLU D 782 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 786 " --> pdb=" O LYS D 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 782 through 786' Processing helix chain 'D' and resid 794 through 819 removed outlier: 4.052A pdb=" N LEU D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 800 " --> pdb=" O PHE D 796 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 5.554A pdb=" N GLY A 16 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 96 " --> pdb=" O LEU A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.569A pdb=" N TYR A 137 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL A 189 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 134 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP A 191 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE A 136 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 221 removed outlier: 3.984A pdb=" N PHE A 241 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN A 220 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 476 through 477 removed outlier: 4.074A pdb=" N GLY A 727 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 728 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.937A pdb=" N ASP A 486 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.632A pdb=" N ALA A 697 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA9, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.104A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 132 through 134 removed outlier: 7.322A pdb=" N PHE B 133 " --> pdb=" O THR B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.511A pdb=" N GLN B 246 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 359 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 338 removed outlier: 3.551A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 502 through 503 removed outlier: 4.004A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 646 through 648 removed outlier: 7.430A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 15 through 18 removed outlier: 5.554A pdb=" N GLY C 16 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 96 " --> pdb=" O LEU C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.568A pdb=" N TYR C 137 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL C 189 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 134 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP C 191 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE C 136 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 216 through 221 removed outlier: 3.984A pdb=" N PHE C 241 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 220 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 336 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 477 removed outlier: 4.074A pdb=" N GLY C 727 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 728 " --> pdb=" O MET C 492 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 486 through 487 removed outlier: 3.937A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.632A pdb=" N ALA C 697 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 500 through 501 Processing sheet with id=AC5, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.104A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 132 through 134 removed outlier: 7.321A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 243 through 246 removed outlier: 3.511A pdb=" N GLN D 246 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 359 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 337 through 338 removed outlier: 3.551A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 502 through 503 removed outlier: 4.003A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 646 through 648 removed outlier: 7.429A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 786 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7912 1.34 - 1.46: 5902 1.46 - 1.58: 11462 1.58 - 1.70: 4 1.70 - 1.82: 200 Bond restraints: 25480 Sorted by residual: bond pdb=" C05 QUS C1301 " pdb=" O19 QUS C1301 " ideal model delta sigma weight residual 1.203 1.450 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C05 QUS A1301 " pdb=" O19 QUS A1301 " ideal model delta sigma weight residual 1.203 1.450 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.203 1.447 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.203 1.447 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C04 QUS B1301 " pdb=" O18 QUS B1301 " ideal model delta sigma weight residual 1.212 1.414 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 25475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 33612 2.62 - 5.23: 701 5.23 - 7.85: 121 7.85 - 10.47: 6 10.47 - 13.09: 4 Bond angle restraints: 34444 Sorted by residual: angle pdb=" N ALA D 786 " pdb=" CA ALA D 786 " pdb=" CB ALA D 786 " ideal model delta sigma weight residual 114.17 108.91 5.26 1.14e+00 7.69e-01 2.13e+01 angle pdb=" N ALA B 786 " pdb=" CA ALA B 786 " pdb=" CB ALA B 786 " ideal model delta sigma weight residual 114.17 108.93 5.24 1.14e+00 7.69e-01 2.11e+01 angle pdb=" C03 QUS C1301 " pdb=" N14 QUS C1301 " pdb=" O20 QUS C1301 " ideal model delta sigma weight residual 112.77 125.86 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C03 QUS A1301 " pdb=" N14 QUS A1301 " pdb=" O20 QUS A1301 " ideal model delta sigma weight residual 112.77 125.58 -12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C LYS C 183 " pdb=" N LYS C 184 " pdb=" CA LYS C 184 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 ... (remaining 34439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 14210 17.26 - 34.53: 790 34.53 - 51.79: 116 51.79 - 69.05: 14 69.05 - 86.31: 20 Dihedral angle restraints: 15150 sinusoidal: 6056 harmonic: 9094 Sorted by residual: dihedral pdb=" CA ASN A 407 " pdb=" C ASN A 407 " pdb=" N ALA A 408 " pdb=" CA ALA A 408 " ideal model delta harmonic sigma weight residual -180.00 -122.01 -57.99 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA ASN C 407 " pdb=" C ASN C 407 " pdb=" N ALA C 408 " pdb=" CA ALA C 408 " ideal model delta harmonic sigma weight residual -180.00 -122.07 -57.93 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLN D 112 " pdb=" C GLN D 112 " pdb=" N MET D 113 " pdb=" CA MET D 113 " ideal model delta harmonic sigma weight residual 180.00 125.61 54.39 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 15147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2641 0.049 - 0.099: 906 0.099 - 0.148: 214 0.148 - 0.198: 21 0.198 - 0.247: 8 Chirality restraints: 3790 Sorted by residual: chirality pdb=" CB ILE C 392 " pdb=" CA ILE C 392 " pdb=" CG1 ILE C 392 " pdb=" CG2 ILE C 392 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A 392 " pdb=" CA ILE A 392 " pdb=" CG1 ILE A 392 " pdb=" CG2 ILE A 392 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C 400 " pdb=" N PRO C 400 " pdb=" C PRO C 400 " pdb=" CB PRO C 400 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3787 not shown) Planarity restraints: 4376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 189 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C VAL A 189 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL A 189 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 190 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 189 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C VAL C 189 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL C 189 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C 190 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 215 " 0.026 2.00e-02 2.50e+03 2.10e-02 6.62e+00 pdb=" CG HIS A 215 " -0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 215 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS A 215 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 215 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 215 " 0.015 2.00e-02 2.50e+03 ... (remaining 4373 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 462 2.61 - 3.18: 25084 3.18 - 3.76: 39721 3.76 - 4.33: 57030 4.33 - 4.90: 85382 Nonbonded interactions: 207679 Sorted by model distance: nonbonded pdb=" O ILE B 612 " pdb=" OG SER B 615 " model vdw 2.038 3.040 nonbonded pdb=" O ILE D 612 " pdb=" OG SER D 615 " model vdw 2.038 3.040 nonbonded pdb=" O ILE C 608 " pdb=" OG SER C 611 " model vdw 2.091 3.040 nonbonded pdb=" O ILE A 608 " pdb=" OG SER A 611 " model vdw 2.092 3.040 nonbonded pdb=" O SER D 64 " pdb=" OG SER D 67 " model vdw 2.099 3.040 ... (remaining 207674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 27.200 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 25488 Z= 0.431 Angle : 0.992 13.086 34460 Z= 0.541 Chirality : 0.051 0.247 3790 Planarity : 0.006 0.060 4376 Dihedral : 11.415 86.314 9318 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 18.36 % Favored : 81.13 % Rotamer: Outliers : 0.23 % Allowed : 4.52 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.98 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.92 (0.12), residues: 3138 helix: -3.08 (0.11), residues: 1092 sheet: -3.74 (0.33), residues: 174 loop : -3.50 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 599 TYR 0.021 0.002 TYR B 469 PHE 0.025 0.003 PHE B 101 TRP 0.019 0.003 TRP D 766 HIS 0.011 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00839 (25480) covalent geometry : angle 0.99180 (34444) SS BOND : bond 0.00836 ( 8) SS BOND : angle 1.47388 ( 16) hydrogen bonds : bond 0.30476 ( 786) hydrogen bonds : angle 9.76133 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9034 (mmm) cc_final: 0.8765 (mmt) REVERT: A 84 MET cc_start: 0.8164 (tmt) cc_final: 0.7931 (tmm) REVERT: A 175 MET cc_start: 0.8960 (mmp) cc_final: 0.8710 (tpp) REVERT: A 271 TRP cc_start: 0.6826 (m100) cc_final: 0.6599 (m-90) REVERT: A 459 MET cc_start: 0.8535 (mpt) cc_final: 0.8282 (mpp) REVERT: A 523 MET cc_start: 0.8402 (tpt) cc_final: 0.8112 (tpt) REVERT: A 666 MET cc_start: 0.9338 (mmt) cc_final: 0.8828 (tpp) REVERT: A 686 MET cc_start: 0.8183 (mtp) cc_final: 0.7593 (mmm) REVERT: A 704 MET cc_start: 0.8882 (ptp) cc_final: 0.8635 (ptp) REVERT: A 785 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5895 (tm) outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.1260 time to fit residues: 6.6456 Evaluate side-chains 29 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.254 Evaluate side-chains 31 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 LYS cc_start: 0.9138 (ptmt) cc_final: 0.8863 (ptmm) REVERT: B 292 MET cc_start: 0.8523 (mpp) cc_final: 0.7990 (mmp) REVERT: B 708 MET cc_start: 0.9203 (mtt) cc_final: 0.8990 (mtp) REVERT: B 721 MET cc_start: 0.9031 (tpp) cc_final: 0.8635 (tpt) REVERT: B 761 LYS cc_start: 0.9439 (mtpt) cc_final: 0.8971 (tptp) REVERT: B 781 LYS cc_start: 0.8432 (pttt) cc_final: 0.8038 (pttm) REVERT: B 807 MET cc_start: 0.8885 (mmt) cc_final: 0.8441 (mmm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1417 time to fit residues: 5.4947 Evaluate side-chains 23 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.0270 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0010 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.0770 overall best weight: 0.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN C 131 GLN C 257 GLN ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN C 638 GLN Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 46 HIS D 93 HIS D 207 GLN D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.043366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034959 restraints weight = 57738.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036137 restraints weight = 37850.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.036938 restraints weight = 27918.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037487 restraints weight = 22430.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.037898 restraints weight = 19109.331| |-----------------------------------------------------------------------------| r_work (final): 0.3002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.040049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.032481 restraints weight = 62817.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.033412 restraints weight = 41794.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.034043 restraints weight = 30861.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.034484 restraints weight = 24829.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034762 restraints weight = 21154.282| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25488 Z= 0.161 Angle : 0.782 10.178 34460 Z= 0.418 Chirality : 0.047 0.176 3790 Planarity : 0.006 0.054 4376 Dihedral : 8.860 81.501 3474 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.38 % Allowed : 15.49 % Favored : 84.13 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.13), residues: 3138 helix: -1.85 (0.13), residues: 1238 sheet: -2.68 (0.35), residues: 176 loop : -3.65 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 599 TYR 0.024 0.002 TYR C 434 PHE 0.019 0.002 PHE A 575 TRP 0.050 0.002 TRP A 602 HIS 0.013 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00321 (25480) covalent geometry : angle 0.78194 (34444) SS BOND : bond 0.00083 ( 8) SS BOND : angle 0.72456 ( 16) hydrogen bonds : bond 0.05185 ( 786) hydrogen bonds : angle 5.93790 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 58 MET cc_start: 0.9343 (mmm) cc_final: 0.8411 (mmm) REVERT: C 666 MET cc_start: 0.8882 (mmt) cc_final: 0.8367 (mtp) REVERT: C 670 MET cc_start: 0.9107 (mtm) cc_final: 0.8357 (mtt) REVERT: C 704 MET cc_start: 0.8868 (ptp) cc_final: 0.8532 (ptm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1257 time to fit residues: 5.1347 Evaluate side-chains 23 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.237 Evaluate side-chains 32 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 MET cc_start: 0.9227 (mtt) cc_final: 0.8735 (mtp) REVERT: D 503 MET cc_start: 0.7739 (ttp) cc_final: 0.7380 (ptm) REVERT: D 721 MET cc_start: 0.8901 (tpp) cc_final: 0.8326 (tpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1163 time to fit residues: 4.8766 Evaluate side-chains 22 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.951 > 50: distance: 0 - 1: 18.120 distance: 0 - 7: 12.757 distance: 2 - 3: 12.732 distance: 3 - 4: 11.854 distance: 4 - 5: 12.624 distance: 4 - 6: 9.199 distance: 7 - 8: 32.413 distance: 8 - 9: 26.157 distance: 8 - 11: 18.183 distance: 9 - 10: 13.887 distance: 9 - 18: 26.652 distance: 11 - 12: 21.413 distance: 12 - 13: 22.690 distance: 13 - 14: 14.597 distance: 14 - 15: 16.538 distance: 15 - 17: 3.331 distance: 18 - 19: 18.448 distance: 19 - 20: 26.731 distance: 19 - 22: 10.321 distance: 20 - 21: 25.068 distance: 20 - 29: 33.706 distance: 22 - 23: 14.171 distance: 23 - 24: 16.881 distance: 24 - 25: 20.716 distance: 25 - 26: 33.873 distance: 26 - 27: 13.072 distance: 26 - 28: 18.636 distance: 29 - 30: 45.024 distance: 30 - 31: 19.770 distance: 30 - 33: 17.828 distance: 31 - 32: 41.993 distance: 31 - 36: 26.608 distance: 33 - 34: 25.041 distance: 33 - 35: 41.057 distance: 36 - 37: 41.162 distance: 37 - 38: 33.564 distance: 37 - 40: 17.235 distance: 38 - 39: 37.660 distance: 38 - 43: 37.129 distance: 40 - 41: 16.646 distance: 40 - 42: 35.502 distance: 43 - 44: 34.692 distance: 44 - 45: 35.289 distance: 44 - 47: 25.203 distance: 45 - 46: 14.646 distance: 45 - 51: 19.900 distance: 47 - 48: 24.503 distance: 48 - 49: 37.682 distance: 51 - 52: 10.142 distance: 52 - 53: 21.537 distance: 52 - 55: 22.508 distance: 53 - 54: 25.899 distance: 53 - 59: 18.743 distance: 55 - 56: 13.514 distance: 56 - 57: 33.060 distance: 57 - 58: 19.317 distance: 59 - 60: 4.576 distance: 60 - 61: 3.253 distance: 60 - 63: 5.997 distance: 61 - 62: 14.150 distance: 61 - 67: 7.655 distance: 63 - 64: 5.454 distance: 64 - 65: 4.449 distance: 64 - 66: 4.395 distance: 67 - 68: 5.241 distance: 68 - 71: 3.151 distance: 69 - 70: 4.109 distance: 69 - 74: 7.108 distance: 71 - 72: 6.410 distance: 71 - 73: 7.071